Applications with GPU support

The following applications have GPU support and can be run on HPC’s GPU cluster. To run these programs on the GPUs, you will need to add the application-specific configuration files to your account’s configuration file.

For accounts using the bash, sh, or ksh shells:

To add GROMACS (4.6.1), add the following line to your account’s .profile:

source /usr/usc/gromacs/4.6.1/setup.sh

To add NAMD 2.9, add the following line to your account’s .profile:

source /usr/usc/NAMD/2.9-gpu/setup.sh

To add Matlab 2013a, add the following line to your account’s .profile:

source /usr/usc/matlab/default/setup.sh

For accounts using the tcsh or csh shells:

To add GROMACS (4.6.1), add the following line to your account’s .login:

source /usr/usc/gromacs/4.6.1/setup.csh

To add NAMD 2.9, add the following line to your account’s .login:

source /usr/usc/NAMD/2.9-gpu/setup.csh

To add Matlab 2013a, add the following line to your account’s .login:

source /usr/usc/matlab/default/setup.csh

Requesting GPU nodes

For details on how to request GPU-enabled nodes in your portable batch system (PBS) script, please see the section on requesting GPU nodes on the following page: Running a Job on HPC using PBS.